Misunderstandings
by Jdragonfire29
Summary: Takes place before season finale. Booth and Bones do 'talk' before they both leave, neither realizing all the misunderstandings that will cause everything to go off track.
1. Chapter 1

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

I stare out the airplane window looking out over the sea and I am unable to stop the flow of flashbacks from last night...

_I am finishing packing up and a knock is at the door with the late hour, I can only assume its Booth. I open it and give a small smirk and whisper Booth he smiles but his head is still facing the ground not looking at me. He suddenly looks up and walks in closing the door behind him._

_There are no words uttered from him, his eyes are burning into me. I see his intentions a second before he steps forward and wraps his arm around my waist and pulls me into a kiss. For the first time in my life, I do not think, I do not analyze, and I just go with it. I deepen the kiss, surprising him and he lets out a soft moan. His lips leave mine and I hear a gasp of surprise and realize it comes from my lips. I want more._

_Booth lowers his head to my neck, nipping and kissing his way down to my collarbone. I pull at his shirt desperate to feel his flesh. His hand grasped the front of my blouse and tears it open. His hands slide around my waist and he kissed his way down my stomach. As he slowly kneels before me, I successfully yank his shirt off. He grinned up at me. My pants were gone and I stood before him in red lace bra and panties. His eyes locked with mine and I pulled him up to me. Our lips met again. The kiss made all thought stop. I knew then that I loved him. This had to be what he was always going on about._

_We kissed our way to my bedroom and I backed him into the bed. Pushing him down and crawling on top of him. I unbuttoned his jeans and pulled them down, slowly kissing my way back up his thighs. My hand slid over briefs stroking his cock through the fabric. He groaned and his head tilted back. I could feel myself getting wetter with each noise he made. He grasped my arms and pulled me up so I my pelvis was pressed to his. We both moaned at the contact and we are lost again in our kiss._

_Booth rolled us so he was on top of me, unclasping my bra and ripped my panties off. My breath hitched, it was such a turn on. He discarded his briefs and settled himself between my legs. Our eyes locks and he slowly slid inside me._

_"Boooth" came my breathless gasp_

_"Bones...my bones." He looked at me and gave a soft smile as he slowly started pace. I was beyond gone. I knew I was close already._

_"Love you." He whispered to me knowing at this point I couldn t run._

_"Booth...love you." Gasped from my lips in a lust frenzied whisper. I could feel Booth shudder and a deep moan left him. His pace immediately picked up. We were both animalistically driving towards climax. Our bodies had taken over as our minds were lost in the lust. We both climaxed and Booth stayed within me. Our eyes locked and I knew I had to say it._

_"I meant it Booth. I do love you." I was petrified of the admission; I was waiting for the pain to come, something to happen as it always has in my life. He smiled his eyes glassy and we kissed again. I felt him harden again and we started all over again. We made love until the early morning hours and both drifted to sleep. When I woke up he was gone. I knew he would be, since he had to check into base the next morning. Yet I missed his company already._

_My body was quivering from _the thoughts, wishing I could be there again. My breath was quick, my pulse racing, I was still amazed I took the leap of faith and told him I loved him. My only hope was I didn t regret it later. I didn t think I could have an open heart and I am hoping that me doing this doesn t ruin me.


	2. Chapter 2

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

As the planned landed in Maluku, I was vaguely aware of Daisy rattling about as usual. How I am going to tolerate her for a year is going to be challenging. I grabbed my carry-on and walked with Daisy off the plane to pick up the rest of our luggage. I pulled out my cell phone turning it on. I admit it; I was hoping that Booth had called to check in with me. No messages. I was acting completely irrational, after all we just saw each other less then twenty four hours ago. I shook off the thought and conversed with Daisy while we awaited our luggage at the carousel.

A few hours of driving and we arrived at our quarters for the dig. I was not as happy as I anticipated being here. This is a monumental dig, this is something others in my field can only dream of and I am the lead. Then why am I just thinking of DC and Booth.

Three weeks have passed and I still have had no communication with Booth. I have sent him several emails and have received no response. No undeliverable messages or read receipts. This is the right email. His old cell number doesn t work he had turned it off knowing he wouldn t need it where he was. Doubt was beginning to set in. Maybe our night together was just closure to him.

The dig is progressing well. Extremely signification research is being done and everything is progressing nicely. It has been two months since my arrival. Still no word from Booth and I am beginning to ignore the doubts. Now it is worry. Maybe something happened to him. I have not been feeling well and I have a feeling my concerns are manifesting into illness. I need to find out where he is. I just need to know he is ok. I finally just decide to pull some strings . I call a few friends at the state department asking them to let me know his status. They promised they would get back to me as soon as they could.

It has been 10 weeks since my arrival. I finally went and saw a doctor since I was still feeling unwell. Daisy had even begun to notice. It was over an hour to a town with a true doctor. They ran a few tests and they had me wait for results. When they came back they said I was pregnant. Now that was unexpected. I had an overwhelming sense of joy and yet at the same time sorrow because I didn't know what happened to Booth. It was not planned but it was just over a year ago that I had been asking Booth to donate so I could be a mother. Angela got her wish, we did it in the messy mind blowing sex way. I couldn't stop the chuckle.

When I arrived back at the dig site there was an envelope in my tent for me. It was from the State department. There was a bunch of photos, I smiled at the first. It was Booth in full gear with other soldiers; he looked to be in good health. I ran my finger along his face on that page. As the shots progressed it showed him interacting with other soldiers. The last two were what made my stomach drop. It was Booth with his arms wrapped around a female soldier. He was smiling at her. The last photo was of them kissing.

I didn t even realize I was crying the tears poured down my face and I roughly sat on my cot. He moved on. There was a note enclosed telling me "Dr. Brennan, Not to worry they would not notify the army of his fraternization since this was technically off the books." That made me cry more.


	3. Chapter 3

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

My work was being done in a daze, I could not concentrate. I put a call into the foundation sponsoring the dig. After explaining my pregnancy and asking them to keep it quiet. I gave them two more months in Maluku and then I was going back to the states. In that moment though, I knew I would not be going to back to DC. They had agreed that I could still oversee the project, if I wished, remotely. Just from the few months I had been here, I had plenty of research to do and write about. We shall see where I stand before I fly back.

The five month mark has arrived. I was on my way to the airport back to the states. My flight came into New York and I caught a connection to San Diego. I decided to go to the west coast. Far away from DC plus I owned a house out there that not many knew of. I wanted someplace peaceful. The house overlooked that water. It had been empty for years. I had made arrangements for someone to go out there last week to clean it and get it ready for my arrival. As the plane landed in San Diego, I swallowed the lump in my throat and held back the tears that were threatening to spill.

Luckily I had arranged a car to pick me up and get my luggage. The chauffeur was very pleasant, I believe he could tell I was unhappy. He walked the luggage up to the house and brought it inside upon our arrival. I signed off on a very large tip, since he made this less painful for me.

I walked around the house, reacquainting myself with it. It most definitely needed furniture, there was mainly just a bed and a few chairs here. I needed to pick up a car, furniture, baby stuff. Most of all at the moment, I wanted Angela. This is the one time in my life where I had to do what Booth and Angela always told me to do admit I needed help and not be alone. I dialed Angela's cell, hoping she would answer.

"Hello?" my eyes involuntarily closed with relief to hear her voice

"Ang?"

"Sweetie! How are you? How is Maluku?" she half screamed with excitement into the phone

"I am in California." I was on the verge of tears and nothing else came out.

"What? Why are you there? Bren you alright?" her voice had turned to concern and that opened the floodgates and I cried. "Bren. Whats wrong?"

"I'm sorry. I didn't mean to frighten you. I left the dig. It's complicated."

"Ookay. Why aren't you in dc then?"

"I am not going back to dc. I am staying in San Diego." I paused to figure out where to start. "I'm pregnant."

"When? How? What?" she was rattling questions

"Ang...it's a long story and I know I have no right to ask this but can you come here. I need you." I shocked myself at the flat out admission and from her silence I knew I surprised her too.

"I will be there as fast as I can. Are you ok? Jack will be with me is that ok?"

"Of course, I am sorry to pull you away but..." I didn t get to finish.

"Stop. Nothing to be sorry for Bren. I will call you back with flight details ok?"

"Thanks Ang."

When I hung up, I felt some relief. I really needed her now.

Less then 24 hours later, Angela and Hodgins were landing in San Diego. I had a car pick them up at the airport to bring them to the house. I was sitting on the porch when they arrived. Angela didn't go for luggage, she just ran up and hugged me, which dissolved me to tears. She ushered me inside and I was vaguely aware of Jack coming in with luggage and sitting across from Ang and I in the living room.

"What is going on Bren?" Ang was being direct knowing I wasn't one for small talk.

"I will leave you two alone." Jack looked unsure if he should stay. I looked at him and remembered our time in that car.

"No stay." They both seemed surprised. "It's ok. You deserve to know I dragged you away from Paris for this." I paused thinking of where to start. "Booth and I slept together the night before we left." Jack and Angela s faces were a combination of shock and joy.

"The baby is Booths then." Jack stated plainly, since Angela seemed to not have gained her voice yet.

"Yes. He does not know."

"I am sure you can get in touch with him" Ang started talking and stopped noticing the look of distress on my face. I couldn't do this.

"Be right back." I went to my room and retrieved the envelope. I walked back to them and handed it to Angela. Jack walked over and looked with her. I think they both thought something happened to him and I felt bad for approaching this in this fashion but it was painful to discuss. I heard a gasp and I knew they got to the last few photos.

"Son of a bitch." Hodgins mumbled with his fist clenched. I had tears down my face again. Angela just started at the picture. I think she was trying as I was thinking there was a better explaination.

"There is a note there too." I laughed tearfully. "He wanted me to open up, give us a chance. I opened myself up to him that night. Even told him I loved him. Wrote him multiple times the first few weeks and nothing, after 10 I was worried. I reached out to a friend at the state department to ensure nothing bad had happened to him. This is what I got back." I walked away from them over to the windows and looked out onto the ocean.

"I don't know what to say Bren." She paused seeming to reach for what to say next. "I am going to kill him."

"No. I just need to move on. I need your help." I smiled at her and Jack. "I want to decorate the place and make it home. I need new furniture, a car, baby stuff, nursery. Lots to do and I really do not want to do it alone, nor do I know where to start. I find I am very overwhelmed." I locked eyes with her. "This is hard for me to ask and I know you are newly married"

"Dr. B. Stop its ok." Jack jumped in before Ang. "We are here for whatever you need." My eyes teared up.

"I think its time you called me Bren or Tempe." I smiled at him and he nodded.

"Sweetie of course we can help you. You are having a baby!" Ang grinned. "I am going to be an Auntie!"

"Actually I wanted both you and Jack to be the godparents." Both smiled and said simultaneously "We would be honored."

"Ok now lets make this house more livable. You seriously need more furniture." Ang was already accessing everything I needed. "How long have you owned this place?"

"Six years or so." Both looked surprised. "I just was too busy and never here."

"No worries we will get you all set up." Ang smiled and Jack just laughed.


	4. Chapter 4

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

Note: Thank you so much for the reviews! Enjoy!

Still no emails, no communication from Booth at all...I do not know why I still check, but I keep hoping for some rational explanation for his behavior. It has been eight months since we have seen each other and nothing. There is no way he didn't hear me admit how I felt.

I am sitting on the back patio off the kitchen listening to the ocean. It is peaceful here. I needed this. Angela and Jack have been amazing. The house looks great. Angela picked the colors, we both shopped for furniture and just a few weeks after they arrived everything was done. Angela was upstairs now painting the nursery. I was not allowed to look, which I find ridiculous since it is my house, but I go along since it is pointless to argue to Ang. Plus I know it not good in my condition to be breathing in all the paint fumes.

I must admit, I loved my new car as well. Jack convinced me to get all the upgrades. It s a Mazda 7 with the Grand Touring Package. Plenty of room for a child and had a very good safety rating.

Jack and Ang bought a house nearby. They were staying. The decided to stay out here with me instead of going back to DC, none of us have reached out to Cam yet to let anyone know our decisions. At this point I am not sure if we are avoiding it because of questions, or if we just are so content that we just keep forgetting.

I see a car pull up, its Jack. I grin as I see the bag of food.

"Hello? Where is everyone at?" He shouts as he enters.

"I am on patio. Ang is still painting." I say with a half pout. I hate surprises. Jack just smiles.

"Well I brought food. Thai." He smiles, the friendship with Jack has grown over the last few months. Him and Ang were fantastic, I do not know what I would have done without them.

"Perfect." I smile back. "I was just thinking we really ought to call Cam and notify her of our intentions. She still believes that I am in Maluku and you in Paris."

"I have thought about that and I have a plan if you are ok with it." He pauses "I am going to go to the board and see about getting another branch of the Jeffersonian here."

"Why would they agree to that?" I am confused and he just rolls his eyes

"Because we are the best team they have ever had, I am a very big contributor. You are the top in your field and they do not want any of us to completely leave."

"I can make a significant donation to help that along then." I smile at him

"I was thinking the same thing. If we both wave money at them plus threat of us leaving, I really can't see them saying no."

"What about FBI involvement? I couldn't hide the apprehension in my voice."

"Once we talk to Cam and get Board approval it will take time to set up here. We can handle west coast issues. We can consult on other cases via webcam. You can say you do not wish to travel to DC unless it is critical and that would be your call on a case by case basis."

"Let's do it."

"Awesome. I gotta go run it by Ang. Eat up. Be right back down." He ran up the stairs to the nursery. I just smiled. This could work new life, I didn t have to give up what I loved. I absentmindedly rubbed my hand on my ever growing stomach.


	5. Chapter 5

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

February 20th at 4:00am, I welcomed a beautiful baby girl Katrina Ruth Brennan. She was a healthy 6 pounds 4 ounces and delivered in ten hours. I was calling her Kat for short. I had originally thought about using Christine in honor of my mother but Ruth was my mothers real name and that seemed appropriate.

Time was passing quickly, Kat was three months old. Over that time, Jack and I had convinced the Board to open a Jeffersonian Division in San Diego. The facility work was being pushed through quickly and should be up and running by end of June. Since the three of us were overseeing everything we made a few changes from the set up in DC. Angela's office was practically a wing. There was plenty of space for her to do art work, a special area for facial reconstruction and to work on her programs pending patent. Jack had set up a separate area for his department, including a safe room for experiments. My office was similar with exception of an area for Kat. We set up a centralized area for arrival of remains. We ordered more equipment then was available to DC office, in anticipation of this being successful. Cam was shocked when we called her. She knew the board had agreed to set up a secondary location but had no idea we were involved. We felt bad keeping her out of the loop but this is how it turned out. We asked for her recommendations for a specialist in her field in California. She promised to get us her list of those she thought might be interested.

Upon opening, I had agreed to teach at our location for top anthropology students. The Jeffersonian was hoping this would create a larger pull to the field and hopefully bring more expertise to the firm.

Everything was working out as the three of us had hoped.

June 6 Washington DC, Coffee Cart outside of Washington Monument stood Seeley Booth waiting for Bones to arrive. He had two cups of coffee in hand. As the hours passed he realized she wasn't coming. Dejected he threw the coffee away and went home. He hadn't even gone to his apartment, he was still in full uniform waiting to see Bones. He had been waiting for this moment for a year.

He walked into his apartment and booted up his computer to check emails. A years worth will take him all night to read. He was waiting till tomorrow to go see Parker. He pressed play on his answering machine and there was a voicemail from Sam. She was finishing her tour and was hoping to get together. Booth s eyes closed, remembering that day.

_They had been under heavy fire, lost a few comrades. He had only been there two months. He was just supposed to go out for training. That s it. How the hell he got pulled into this, he would never know. Only Sam and him made it back to camp. Both were grieving the loss of their platoon. Next thing he knew they were in bed. He had no access to emails or phone was unable to reach Bones. He wasn t thinking straight and he hoped to hell she never found out. Maybe she moved on. All he knew was that he royally fucked up._

He deleted the message no that was there. He was home. He wanted Bones. He pulled up his email account. There were more then he thought. He sorted them by sender and found the ones from Bones. His face lit up. He decided to start at the oldest and work his way to present.

_June 7, 2010 "Booth, I miss you already. I cannot believe we will not see each other for a year. I am now doubting my decision to go with exception of you wouldn t be in DC either. Write soon. Love, Bones."_

_June 9, 2010 "Booth, I hope you arrived ok there and all is well. I haven t heard from you and I know it is irrational but I am beginning to worry. Please contact me soon. Love, Bones."_

_June 14, 2010 "Booth, I feel I am writing too much but I find that I cannot help myself it makes me feel better talking to you. The dig is going well, this is a very significant find. I am excited to be participating. I hope you are well. Love, Bones."_

_June 26, 2010 "Booth, I still have not heard from you. I am not getting delivery failures so I must assume these emails are going through. I am wondering if you were just thinking of that night as closure and decided to move on. Bones."_

_July 14, 2010 "Booth, I cannot wait to hear from you any longer, I have decided to use my connections as you once put it to find out if you are ok. I am very worried now. I need to know. I will not write more until I hear back, there seems to be no point since I never get a response. Sorry. Bones"_

_August 10, 2010 "Booth, I have my answer now. You have moved on. I am happy you are not hurt. I wish you well. Dr. Temperance Brennan."_

By the time Booth got to the last email he was panicked. She knew! I will go to the Jeffersonian and beg until she talks to me. What have I done?


	6. Chapter 6

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

I could not sleep. I just kept re-reading all of Bones emails. As soon as the sun was up, I showered and dressed. First stop The Jeffersonian.

As I walked in, I had no idea what to expect. When I walked up to the platform, I stopped at the base of the stairs so not to set off the alarm. I no longer had a badge; I had turned it in before I left. Cam was leaned over a body.

"Camile." She looked up surprised.

"Seeley. You're back."

"Don't call me Seeley." I smiled at her

"Then don't call me Camile." She swiped her card stepped down off the platform and hugged me. "How are you? When did you get back?"

"Yesterday actually." I hesitated "How is everything here?" she looked at me with a raised brow.

"What's wrong?"

"Nothing, just stopping in to say hi" she looked at me and knew I was lying "I messed up Cam. I really need to talk to Bones, but I am not sure how to approach her."

"Um well...okay then." She was looking at everything but me. "When is the last time you talked to her?"

"Why?" I didn't answer her because I just wanted to find out why she said that. Something was wrong.

"She isn't here." Her voice sounded grim

"Bones still in Maluku?"

"No. She isn t, but she isn't in DC either." I could tell Cam was struggling like she didn t feel this was her place to say. I ignored and walked towards Bone s office. When I got there nothing could have prepared me for what I saw. Her name was gone from the door and all her things were gone.

"Is her stuff in storage from before she left?" I was starting to panic.

"No...she left DC. She isn't coming back." I just sat hard on the couch still in her office. This was all my fault.

"Do you know where she is?"

"Seeley, she moved away. She is still working for the Jeffersonian, just not at this Division."

"This is the only Division." I responded confused.

"Not anymore, they opened another one after very persuasive conversations with two donors." She paused to watch his reaction. "Dr. Brennan is now working with the other Division. Only on high profile cases with FBI or if something specific to her expertise is needed. She has agreed to only work remotely with us here and will not come to dc unless it is proven to her that it is important enough to justify her flying out."

"What? When did this happen?" I could feel the anger and embarrassment at this mess. All this was my fault.

"I do not know when she moved. The new division will be opening up end of this month."

"Where is the opening?"

"Booth, I am under orders not to disclose Dr. Brennan's location. You are not permitted at the new division offices." She paused and placed her hand on my leg. "What happened?"

"I messed up Cam." I put my head in my hands trying to clear my thoughts. "The night before we left, we slept together." I looked up at her.

"Oh. Oh boy." Cam s eyes were big as saucers with surprise. "Was it bad?"

"No! No no. God no. She even told me she loved me. I left in the morning while she was sleeping, which she knew because I had to be to base early. We had agreed the night prior to keep in touch. Also agreed to meet at our spot new Washington Monument after a year." I shook my head. "When I agreed to this, I agreed to train new soldiers. They lied. I got shipped out to a base in Afghanistan and I trained but I was also engaging in live combat." Cam's eyes softened, knowing I never would have gone if that were the case. "I didn't have access to communications where we were. About 8 weeks into the tour, we were sent out on a mission and came under heavy fire. Only two people from my group survived. Myself and Sam we talked and comforted each other the night we got back to base. She was there she knew. I wasn't thinking. I slept with her." I looked at her and I could see the disapproval but also understanding in her eyes. "Bones was worried and from what I gathered from her emails, she did what I always told her to do. Use her connections. She called the State Department and had them check to ensure I was safe. I don't know what they told her or she saw, but in her email she said 'I have my answer. You have moved on.' " My eyes teared up. "She wrote me every couple days then it turned to every week. She was worried, I had no way of contacting her. I don't know what she was thinking but even if I could argue with her that it wasn't my fault for no communication. I cannot argue the fact that I did sleep with another woman."

"Seeley. Dr. Brennan is very rational and logical. If you could explain, she might listen to you." I looked at her skeptically. "Hey, you wont know till you try. We reactivated her Jeffersonian email. It hasn t changed. Email her."

With that Cam got up and walked away from me. I just sat in Bones office a bit longer. It seemed so empty without her here.

/

After I left the Jeffersonian, I went to visit with Parker. He was distant from me. Angry as well with no contact, now I had two people I needed to make this all up to. I have a feeling Parker is going to be the easier of the two. Rebecca seemed happy I was back. She said I could have Parker this coming weekend. That gave me time to go to the bureau and find out about getting back to work.


	7. Chapter 7

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

We were all at the new facility together. We needed to come in to check everything to make sure it was adequately prepared to open in two weeks. It also gave me time to get my office set up. Kat was sound asleep in my arms. As I went into the office, I could see Angela had already been here. I couldn't help but smile. To the left of my desk was a playpen with a mobile hanging over it, a bassinet and the wall behind it was painted with a mosaic. Not the most appropriate thing for an office but I guess neither was having my daughter in it. As Hodgins so happily stated, we funded it, our rules.

I placed Kat down in the bassinet and turned back to my office space. Everything was almost identical to the way it was in DC. Cam had delivered all my office items here, plus I brought a box from home. I slowly unpacked. After I put away everything from DC, I started to put out everything from the home box. Pictures...something I did not do in DC. I wanted the personal touches to soften the work space. Kat had changed me. I had a picture of her and me on my desk from the day she was born. Another with Jack and Angela holding her, the last one...was of me swinging in hammock in back yard with Kat sprawled across my stomach. Angela had taken that picture and given it to me already framed. I loved it.

I booted up my computer to set up my files and email. Apparently they reactivated my old account; there was a large amount of emails in here. Kat was still sleeping soundly, so I started through them one by one. I had sorted it from oldest to newest, hoping I could mainly just delete them. Nothing could have prepared me for the last email Booth.

_"Bones,_

_I know you are angry with me. We need to talk about this. There is an explanation for my lack of contact. Can we please talk? Call you? Meet?_

_There are not the words for how sorry I am._

_Please Temperance_

_Booth"_

I didn t realize, I was crying as I read it.

"Sweetie? What s wrong?" Angela's voice shook me out of my shock. I just pointed her to the computer screen. She read the email. "Are you going to talk to him?"

I was surprised by her directness but I guess she knew I needed it.

"No." The answer came without hesitation. "Nothing he can say will make up for the fact that he was with that woman."

Angela didn t push. She just nodded and walked over to check on Kat. I hit reply.

_"Agent Booth,_

_Unless there is a case, there is nothing that is in need of discussion. I am relieved you are back safe._

_Good luck in your endeavors._

_Dr. Temperance Brennan"_

I hit send.


	8. Chapter 8

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

My heart sank as I read the reply from Bones. I knew she would be stubborn, but hoped she would agree to talk. Now I just needed to determine my next steps. I cannot let this go. I have been in love with her since the day I met her.

Number one, I cannot push or I will literally push her further away. Two, I cannot just show up at her door expecting her to just fold and talk to me. Three, I had no clue what to do next.

/

I had Parker last night, it was awkward at first. He was being distant. As the night went on I got him to talk to me more. Once I asked him about what he did and how school was he was talking a mile a minute. One key word stuck out, well actually two Dr. Bones. Apparently Bones had been exchanging emails with Parker since I left. She helped him with school projects, told him about the dig, his face lit up talking about her. Seeing and hearing that made my heart ache more. Especially when he said he was sad that Dr. Bones wouldn't be nearby anymore. He already knew she moved away.

Gotta leave it to Bones, when she does something she covers all her bases.

/

It has been two weeks since I have been home; I am officially back with FBI full time and working in conjunction with the Jeffersonian. I am hoping that a case comes up that will get me working with Bones again...even if just through webcam. As soon as the thought came, I received a call about a body found in a tunnel by construction workers. I called Cam and asked team to meet me at site.

Cam, Hodgins and Wendall came. It was odd being there without Bones. They did their thing and I had everything shipped back to the Jeffersonian. Within a few hours it was determined that the body had been there for an estimated 2 years. Victim was 30-35 years of age. As the days passed and the team investigated they were able to get identity based on dentals. The case felt like it was slow moving.

Another body was found 2 days, later further down the same tunnel. That body was determined to have been there 1 to 2 years. Construction was halted on tunnel and ever square inch was being searched.

I had a feeling we had come across a serial killers dumping grounds. Cam and Wendall had discussed case with Bones, but I was not included. Finally it was to the point where I needed to talk to her. Cam set me up in Bones old office for privacy knowing this might not go well.

The webcam booted up and there she was. God she was gorgeous.

"Bones?" I smiled hesitantly at her.

"Agent Booth." She gave a small nod, she was distant. "I have reviewed the findings from Cam and Wendall. There are similarities between the method of killings for the two bodies found so far. It would be unwise to assume that it is serial killings until more bodies are found and more conclusive information is obtained."

"Yes, you are right. The FBI has asked me to see if you are able to come her to oversee the investigation in search of more remains?" I was trying to keep the hope out of my voice. She hesitated before answering.

"Wendall and Nigel Murray are more then adequate to deal with that. They are able to coordinate with me here. At this juncture, I do not see a need for me to go to DC." I didn t say anything, I was hoping she was going to say more and thankfully she did. "If any more remains are found and the Jeffersonian feels it would be prudent of me after clear proof, I will consider traveling."

"Ok. Thank you." I paused unsure how to start. "Bones, can we talk? Please? There was a legitimate reason for me not being in contact with you." She was about to interrupt but I kept talking. "I was moved to a new location on mission, outside of the promised scope of training. There was no communication allowed or possible. I didn't contact Parker either."

"This has nothing to do with the current case. I would appreciate if we kept away from personal matters. In response to your statement, I realize you were sent to a different area...I found that out later. Also a few months back, Parker told me of your lack of contact."

"Then you believe me. I wanted to contact you. God Bones, I love you." I was to the point of pleading. Her face turned to stone but her eyes were glassy with tears.

"Yes, you loved me so much you went off and fucked the first woman you came into contact with." My mouth dropped open at the abruptness of her statement and finally the black screen in front of me. I sat in her office unsure of what to do next. My first thought was to call Angela but I wasn't sure that would go any better. At this point though, I didn't think I had much of a choice.

/

I reached for my cell and dialed Ang. She answered on the first ring.

"Angela Hodgins" I couldn't help but smile, almost forgetting they had married before I left.

"Angela its Booth. Please don't hang up." All I got was silence. "I just talked to Bones and it didn't go well. I am not sure how to fix this."

"You are kidding right? There is no way to fix this. You.." her voice was frustrated as she was trying to find the words to yell at me. "you broke her. She opened up to you and you just spit it back in her face. What in the hell were you thinking?" the venom in her voice was unmistakable. Already I knew this was a really bad idea.

"Ang wait I didn't, no I did. Ok I fucked up but I do love her. I really need to figure out a way to fix this to have her listen to me."

"I honestly do not see that happening. Pictures are worth a thousand words. The pictures were the last straw."

"What pictures?" my voice was but a angry whisper and Angela laughed in response

"If you are going to cheat or throw away a relationship, maybe you should think about who could be watching. Funny thing is when she called the State Department she did it because she was worried about you. When she got those pictures with the note of 'don't worry no charges will be pressed since this is off the record' or something along those lines. My first thought was screw him. You know what hers were. No Parker needs him." She hesitated and the last thing she said before hanging up on me was "Don't call me again."

How in the hell did all this spiral so far out of my control. I have lost her.


	9. Chapter 9

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

Livid does not adequately describe how I felt at the moment I disconnected the call with Booth. I did not even mean to have the response I did. My eyes were tearing up and my chest felt heavy. I got up and closed the blinds to my office. Kat was sleeping soundly in her bassinet. I could not hold back the tears. It was physically painful to see him. In my mind I saw a flash of that picture of him kissing that woman. He looked happy. I think that is what truly hurt.

I sat on my couch and let myself cry. I was beginning to believe that I had made a mistake. I could not do this, work with him and not have it effect me.

I heard the key in my door. Angela let herself in and locked the door again behind her.

"Sweetie it's ok." She sat down next to me and put her hand on mine. In that instant I knew she was aware of my conversation with Booth.

"How?"

"Booth called me and told me." She looked apologetic at me. "I let him have it."

"Why would he call you? That is not logical." She smiled at my statement

"Because he wanted to explain to me, hoping I would talk you into talking to him. It's guy logic sweetie."

We just sat after that, nothing said. She let me cry, Kat continued to sleep and both of us were just lost in thought.

/

Two days passed and Cam called me this time.

"Dr. Brennan, recent developments have made it necessary to request you to come to DC." Cam seemed hesitant but direct, before I could reply she explained. "Another two bodies were found, they were placed in same area of tunnel we discovered the first body. This guy is messing with us. We need your expertise to solve this expeditiously."

I hesitated. I did not want to leave Kat. Honestly, I also didn't want to face Booth.

"I will make arrangements to come there. I do request that Agent Booth is not notified."

"Agreed, I will see you soon." With that Cam hung up.

It took me a few hours, but I made arrangements for Kat to be with Angela and Jack. They both expressed concern with me going but knew I was required. Jack offered to accompany me but I honestly told them I would feel better with both of them watching out for Kat. I was finding the idea of being away from her difficult. My flight left in 3 hours. I was packed and Jack was going to drop me at the airport. Before I boarded, Jack gave me a hug and told me to call him or Ang whenever and for whatever. I smiled at him and told him to watch Kat.

As the plane took off my mind was trying to come up with all scenarios of how to handle this situation. I needed to be focused and to get this taken care of quickly. By the time the flight was over, I had multiple plans of action and hoped I was prepared for what was to come.

/

At 4:00 pm on July 8th, I walked into the Jeffersonian. Cam immediately walked over to me and gave me a hug, which I returned not realizing how much I missed her.

"Good to have you here." She smiled.

"Thank you. Good to see you too." I smiled back at her. She looked surprise at my ease. I admit the last year had changed me. "Where are Wendall and Nigel?

"Bone storage. We have the bodies laid out in there."

"Perfect. I will go catch up with them." I made my way to Bone storage. My two previous interns were both studiously focused on the remains before them.

"Findings?" I smiled at them.

"Dr. Brennan?" They both said simulataniously. "Good to have you back."

"Good to see you both. Let s get this solved, shall we?"

Over the course of the next 15 hours we walked through each bone on the remains.

/

At 7:00 am I walked out of Bone Storage with Wendall and Nigel to find Cam. I had no idea Booth was already talking to her. I pulled myself together, immediately locked eyes with Cam and just recited the findings.

"Based on the markings and analysis from Hodgins on the metal in the bone curf marks. I had identified the weapon. It was an Hunga Munga, which was an ancient African tribal weapon. It is a handheld weapon and contains a metal pointed blade with a curved back section and a separate spike near the handle. This is very efficient and causes deep wounds, typically resulting in death. This is not an easy weapon to obtain. I have asked Hodgins to try and carbon date the weapon based upon the metal samples we obtained in the wounds."

"Excellent." Cam eyes shifted from Booth to myself, I could tell she was uncomfortable.

"Wendall and Nigel need to go home and get some rest." Both looked at me surprised, not used to me requiring this. "I have a few more items that I wish to look into and coordinate with Hodgins on. Once I am done, if you are alright with it Cam, I plan to just lay down on the couch in my old office and get some sleep?"

"That sounds reasonable. Thank you." Cam eyes showed surprise but she just smiled.

I gave no indication toward Booth, who continued to stand there awkwardly.

"Wendall. Nigel. Get some rest. I will see you later this afternoon?" They both nodded to me. "Thank you for your assistance. You work was very well done." They both smiled. I turned and went back to bone storage. Mentally trying to prepare myself for Booth who I knew would come storming down to talk to me.

/

Authors Note: The weapon I referenced is an actual weapon, you can google it. I know the name sounds made up :)


	10. Chapter 10

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

I sat there in Cam's office unable to move. My first thought was she looked fantastic, she was wearing a summer dress that hugged her body. Her hair was longer. What really stuck out was she didn't even acknowledge that I was here. As she told Cam about the weapon identification, I just stared at her. Still shocked that she was here, when she mentioned for Wendall and Nigel to get rest my mind just stopped. As she walked away to Bone storage it took a few minutes for my brain to catch up.

"Booth?" Cam's voice pulled me out of my fog.

"She's changed." I whispered. Cam just continued to look at me. "Also she didn't even look at me."

"What did you expect Seeley and you are right, she has changed. My advice... do not be reactive here." I looked at her trying to figure out what to do. I just hopped up and started towards bone storage before I was completely out of Cam's office, I heard her mutter. "Idiot." I continued on my way to bone storage.

I walked in and she was there examining one of the victims bones. I decided to play this her way.

"Dr. Brennan?" She looked up at me. That worked I at least got her to acknowledge me.

"Agent Booth." She turned her eyes back to the bone.

"Have you heard anything more from Hodgins on the carbon dating of the weapon?"

"No and since it is only 2 am, I assume he is sleeping and will not be to it for a few hours." Her tone took on an aggravated tone.

"This is a murder investigation, I assumed he was working now." She stopped what she was doing and her eyes bore into me.

"What do you want Agent Booth? You know from what I just told Cam that I recently requested the carbon dating. You are fishing for information."

I was surprised by her being able to read me and also by her actually continuing the conversation.

"What do you think Bones? I want to talk to you. We need to talk." I looked to her pleadingly.

"I believe we discussed everything yesterday. Did we not."

"No, we did not. You hung up on me, after yelling at me." I took a breath. "Rationally speaking that would conclude that the conversation was ceased by you and we were unable to finish it." I was praying logic was the way to go here.

"While I appreciate you effort to try and co hearse me into having this discussion with you, I assure you there is nothing more to discuss." Her tone was beginning to have a warning edge to it.

"No, there is plenty to discuss. Bones. I love you. I still love you." I saw a flicker in her eyes. "I messed up, I admit to that. I regret it more then I can express." Her eyes started to tear up and I felt like a bigger schmuck then before. "Please let's talk and see if we can work through this?"

"You have broken any trust or love that I had for you. I opened myself fully to you and you rejected it." Her voice was thick cracked and was thick with emotion.

"No. God no...I didn't reject it." I looked at her, she was trying very hard to not cry. "I was beyond happy when I heard you say you loved me that night. I wanted to stay, I did not want to leave you."

"You did and I was ok with that, although that was under the impression that we were both on the same page. You obviously were not." Her voice continued to be thick with emotion and a few stray tears fell from her eyes. My heart ached watching her in such pain, especially knowing I was the cause of it.

"Temperance, I need to explain. What you saw was a mistake." I paused trying to come up with the proper words.

"No. What I saw was proof of my err in judgment." With that she turned and ran from the room. Leaving me to stand there wondering how in the hell I was going to fix this.


	11. Chapter 11

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

A/N: Sorry for delay in posting. I had a very close friend of mine die last week and then this week was my move. It has been a very insane two weeks. Thank you again for all the reviews.

**************  
_Brennan Point of View_

As I walked out of bone storage, I decided I didn't want to stay in my office. I grabbed my bags and left. Luckily I was able to grab a taxi before anyone could stop me. I had them take me to the JW Marriot. I was happy they had a suite available. As soon as I entered the room the tears fell.

My cell had rang multiple times but I refused to answer. I needed time alone. I ran a hot bubble bath and just tried to unwind. Of course not twenty minutes into my bath there was incessant knocking on the door. I got up and grabbed a robe. I was soaking wet and covered in suds. I didn't ask who it was, I just opened the door...

"Booth! What in the hell are you doing here?"

"We need to finish our talk."

"No, we really do not." I went to close the door but he blocked it and pushed his way in. "What the hell! How did you find me here?"

"FBI Bones. I checked your credit card activity." He looked ashamed and proud all at once.

"You had no right to do that. It was abusing your privileges with the bureau. I should notify Cullen."

"Stop...ok just stop. We need to talk and I do not need you running." He looked at me again pleading. "Do you want to change?"

"Why? Does my robe bother you?"

"No. Just wanted you to be comfortable, it's all wet."

"Obviously...I was enjoying a hot bath when you barged in!" I huffed and walked over to the bar and pulled out a bottle of wine. "Fine. You are here. Talk."

*******************  
_Booth Point of View_

I could not believe she just walked out. Shit! I stood for a second trying to think of what to say in response. Screw it. I ran over to her office and found it empty. She was nowhere to be seen. No she is not getting out of this argument. We need to talk. I smiled and headed to Hoover. Two hours later after breaking a few rules, I found her hotel. I knocked and there was no answer, so I am just going to continue to knock till she does.

I hear a huff and the door open. She looks gorgeous. Her hair is soaked the bath robe is wet and clinging to her.

"Booth! What in the hell are you doing here?" She was beautiful when she was angry.

"We need to finish our talk." I was trying to be calm.

"No..we really do not." She went to close the door and I blocked pushing my way in. "What the hell! How did you find me here?"

"FBI Bones. I checked your credit card activity." I was ashamed and proud all at once. She should have known I would.

"You had no right to do that. It was abusing your privileges with the bureau. I should notify Cullen."

"Stop...ok just stop. We need to talk and I do not need you running." I ran my fingers through my hair, frustrated. "Do you want to change?"

"Why? Does my robe bother you?" Hell yes it does she look fantastic.

"No. Just wanted you to be comfortable, it's all wet." I was lying through my teeth!

"Obviously I was enjoying a hot bath when you barged in!" She huffed and walked over to the bar and pulled out a bottle of wine. "Fine. You are here. Talk." I had no idea where to begin or what to say. "Fine. I will talk. Who was she?"

My eyes I knew had widened at the question. She went straight for the throat.

"A member of the team I led on a mission." I paused trying to think of where to explain from here.

"Was she worth it?" She asked me with such disappointment in her voice the shame I felt was ten times worse.

"No. God no. It was a mistake. A huge mistake." I tried to convey my seriousness and truth in my face.

"Then why?" Her voice was once again wavering.

"We went on a mission, full team. She and I were the only ones who made it back." I looked down and then back at her. "We were both blindly comforting each other. I knew right after I snapped out of it and knew it was wrong. I was not supposed to be in combat! I was there to train, that was what I agreed to." I was raising my voice but I was angry too. "They were just kids."

She was crying now. She turned away from me and I could see her taking a large drink of the wine she had poured. Her voice surprised me and I didn't expect what she said.

"You are correct. That is not what you agreed to and you should not have been put in that situation." She turned to look at me, her eyes bore into mine. "But that does not excuse your actions."

"Listen Bones...I know it doesn't. I am not making excuses. I am explaining." I walked towards her hoping she didn't either run or deck me. "I still love you just as much as I did before I left." I could see the doubt in her face. "I need you. I need us. Please let's just try and work through this."

She didn t say anything. She just continued to stare at me. I felt like a pile of bones she was examining on a table. I didn t look away, I held my gaze hoping she would see my intentions were truthful.

"If you are looking for an answer right now, I cannot do that. A great deal has occurred since you left and I need to think about this. I have a life that I love now in California. I will not come back to DC." My heart dropped at her words. I can t just run off to California because of Parker. Also the bureau, no idea if they would even let me transfer. Screw it I need to try something, maybe I can work something out with Rebecca.

"Ok. Well I can see about going to California." She looked shocked. "I would just need to work something out with Rebecca."

"What? Why would you do that?" I smiled at her

"I love you Bones. I will not give up on us." I bravely took her hand. "I screwed up, I know that but I know this is right. You are who I want you are the only one I want. I need to follow this through and try and make us work."

"There is not guarantee that it will work. I still do not know how to trust you again." She had tears in her eyes and her voice was thick with emotion.

"I know. I want to try and earn your trust back...please?" She didn t say anything. She just continued to stare at me.

"I cannot answer you right now. I need to think." She walked to her suite door, opening it. "I need you to go." I didn't want to push my luck here, she agreed to think that is better then nothing.

"Ok. Thanks Bones." I walked out the door resisting the urge to kiss her. She closed it behind me and I heard her sobbing. My heart was breaking from this. I caused her so much pain and I always said I wouldn t cause her any. I just had to hope and pray that this was going to all work out.


	12. Chapter 12

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

A/N: Thank you for condolence notes, it has been a rough week. I have this whole story plotted out though, so be patient. I plan to finish. I know this is a short chapter but I wanted to give a feel for after effect of talk before we dive into the next day.

_/_

_Brennan Point of View_

Once the door shut, I walked back to the bathroom and drained the tub, refilled it again with more hot water and bubble bath. I discarded my robe and hung it up on the hook. It was soaked. I then went back and grabbed the bottle of wine, my glass and filled it placing it on the edge of the soaking tub. If I was stressed and upset before I got here, it was ten fold now. I slowly lowered myself into the steaming water. I saw slowly sipped the wine, while my mind was ravenously running through the conversation I just had with Booth.

I knew I was crying, I could feel the tears trailing down my face. I never expected him to offer to go to California...not with Parker being here. I have no idea how to feel about any of this. I never wanted to come back to DC and here I was back where this all began. Booth pleading with me to understand his indiscretion. To forgive to start over...unbeknownst to him the ramifications of our night together made that impossible. I would not trade Kat for anything. She is the single most important thing in my life. She is what has changed me, far beyond the effect Booth himself had on me.

The whole encounter with Booth rattled me. He wanted to work this all out. That would mean telling him about Kat. I am not sure I trust him with her yet. Will he break her heart like he did mine? She is in a stable environment. She is happy. Although logically I know she would be happy with a father, but I cannot help my distrust of him. I keep running his explaination through my head and I logically understand the words...but also am hurt because that is not Booth. Him and his high moral standards he always spouted and he broke them at his first opportunity.

The water is now cold, the wine glass is empty. My thoughts are still jumbled. I am left just as confused as I started. My first instinct is to protect my daughter. A ramification of his betrayal to me, tells me to keep her a away from him...

/

_Booths Point of View_

I left the hotel and drove home. Even though I was finally able to speak with her, the only thing that was echoing in my head was her sobs after the door closed. I had truly broken her and it felt as though any chance of anything more with her. How the fuck did I let this happen?

I need to pray that she is actually going to think about this and not run...


	13. Chapter 13

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

_Brennan POV_

The shrilling of my cell phone woke me, I groggily reached for it.

"Ello?"

"Bren?" It was Jack.

"Yeah...sorry didn't get much sleep."

"You okay?" I could hear the concern in his voice, he was getting far too good at reading me. He was worse then Angela.

"No but I will be once I get home. Had a talk with Booth last and it was interesting to say the least."

"Ookay. Want to elaborate on that?"

"Nope. I can tell you when I get home. Sooner we solve this the better."

"Well then this might help. I carbon dated the metal fragment that was found it was an authentic piece, 18th century."

"Great! I will let Cam know."

"Already emailed both of you, I just wanted to call to check on you. Once again I ask if you need me out there?" I smiled at his offer.

"I will be alright. I need to get ready and get myself back into the lab. I didn't expect to even get a room, but I needed to get away from Booth."

"That worked well." Jack laughed

"Sarcasm isn't good first thing in the morning Jack." Irritated that he was right, it was a mess.

"Seriously Bren, if you need me out there call me, ok?"

"I will. Thanks Jack." With that I hung up.

An hour later, I walked through the doors of the Jeffersonian again. Still felt very surreal. I was silently wishing that Booth was not there already. I needed to get this case solved, so I could get out of here. With the information Jack was able to get us; we identified about a dozen possible dealers who would have sold this weapon. We forwarded the list to Booth. About 20 minutes after Cam emailed him the list, he showed up in my old office.

"Heya Bones."

"Agent Booth, did you get the list from Cam?" I could see he was unsettled by me calling him Agent Booth, but I needed to be detached.

"Yes, I wanted to stop by and take you with me to investigate."

"No, thank you." I turned back to my work.

"Bones, come on this is what we do." His voice took a pleading tone.

"I am no longer involved in field work. My place is in the lab."

He didn't respond after that, but I could feel his eyes on me before he finally turned and left without a word.

/

_Booth POV_

Dammit! She said no. I thought for sure if I could get her in the field and we did our thing it would help. She was not having it. Not even a glimmer of want when I asked. Damn!

It took me half the day to go through all the dealer leads. One finally panned out and of course it was the second to last on the list. They gave me a name and luckily had a surveillance camera too. We finally caught a break. A copy of the tape was send to Jeffersonian and an hour later, thanks to Angela's facial recognition software, we had a match. Brett Stevens. He had a long criminal history, no recent known address but a few old affiliates on here that might be helpful. A full team from the bureau was sent out to track him down.

I was happy to get a break in the case but panicked because that meant she would leave soon.

/

Brennan POV

Cam updated me that they had a name and solid leads, so I told her I would be on my way back home. She looked startled that I didn't want to stay longer but seemed to let it go. I immediately went back to the hotel, packed what I had and went straight to the airport.

Booth would be angry. Hell he would be furious that I just took off, but right now I really didn't care. In less than 6 hours, I would be back home with Kat, Angela and Jack. I could not hide the joy in that statement.

/

_Booth POV_

We got him! One of the teams picked him up. It was perfect. He had effects of some of victims on him. I went back to Jeffersonian to tell everyone the good news.

"We got him." I smiled at Cam, Wendal and Nigel

"That's great Agent Booth." Wendal quickly replied to me. Something was off.

"Where's Bones? I wanted to celebrate and take her to founding fathers for a drink."

"She left." Cam had a sorry tone.

"Back to hotel?" I asked hoping she was not about to say what I was afraid of.

"No she flew back home." I felt the breath leave my lungs. I saw Wendal and Nigel leave me alone with Cam. "I am sorry Booth."

"When did she leave here? Maybe I can catch her?"

"She left as soon as you told us you had a name. She felt there was no longer a need for her here."

"Oh." My chest tightened.

She ran.


	14. Chapter 14

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

_Brennan POV_

I cannot believe I am standing here. I am standing at Booth's door. I missed my flight because I knew I had to tell him. It wasn't right to keep her from him, but I had no idea what I would say. The lights to his apartment were out. Maybe he was sleeping or I was hopeful he wasn't here so I could run back to the airport and forget this whole idea.

"Bones?" Shit! He startled me. "Cam said you left."

"I still plan to, but we need to tell you something before I leave."

"Oh. Okay." He fumbled for his keys and opened the door. "Come in. Let s now give the neighbors anything to talk about." He was trying to lighten the mood with humor but that didn t make me calmer. I walked in and he motioned for me to sit. "Drink?"

"Yes. Water." I heard him in the kitchen, getting the drinks. Too soon he was back in the living room sitting awkwardly on the opposite side of the couch. I took a sip and decided to just dive right into the conversation.

"Booth, I am not sure I will ever forgive you for what occurred." He opened his mouth to talk and I raised my hand. "No. Let me finish. I have to get this out." He just nodded. "I cannot express to you how much that night meant to me." I could hear the emotion in my voice, it cracked and my throat suddenly felt tight. This was a bad idea. "I had thought it was finally what you were always rambling on about. That breaking laws of physics love between two people. I cannot regret that night even though it was not a happy ever after ending as you would put it." He looked upset and was restraining from arguing my point of view. "The reason I cannot regret that night was because the single most important thing in my life came of it...our daughter." He looked even more upset and his eyes were wide. "She deserves to know her father and it is not right for me to not tell you...even though I am angry with you."

/

_Booths Point of View_

I did' t hear her right. Did she say our daughter? Oh god she was pregnant from that night.

"Daughter?" My voice came out in a pained whisper. She nodded and dug through her bag, handing something to me. I took it and saw a picture of the most beautiful thing in the world. A little girl, a few months old, cradled in Bones arms. I couldn't stop the tears that fell. She was gorgeous, just like Bones.

"She's beautiful. What did you name her, when was she born?"

"February 20th at 4 am, she was 6 pounds and 4 ounces. I named her Katrina Ruth Brennan, but I call her Kat."

"I need to see her." I looked up from the picture and looked at Bones hoping that was her intention.

"I know. You can arrange to fly out and visit at some point."

"This weekend?" She looked surprised at the quickness of my response. Technically the weekend was tomorrow.

"I guess so. I am in San Diego. There are multiple hotels you can stay at nearby. I am sorry but I am not ready or comfortable to have you stay with me." I nodded understanding. "I have to go."

"What? Wait." I was surprised by the sudden turn of her leaving.

"Booth, I have a flight out in less than two hours. I will not miss this one. I miss my family." I felt like she had slapped me. Missed her family that did not include me is how I took it. "Call me when you arrive." She just handed me her number and left. I didn't see her to the door. I just sat back down on the couch and stared at the photo of Bones and Kat. I knew I had messed up before and was completely at a loss for how to mend things with Bones, but now I know I screwed up beyond repair. The ramification of that, is the loss of a family I could have had with her together. I gave in and cried.


	15. Chapter 15

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

A/N: Sorry for delay, my move was this weekend and it was insane. Enjoy!

/

Brennan POV

I left his house, started the car and headed to airport. I needed to drop rental and catch my flight in less the 2 hours. I was a few blocks from Booths when bright headlights came into my rearview. They rammed my bumper. I was trying to get away. I decided to circle the block so I passed back in front of Booths. I grabbed my phone and hit speed dial.

"Bones?"

"Booth! I am being chased." I was having a great amount of difficulty getting them off me. They were now next to the car. My mind kept thinking of Kat.

"What?" I could hear the panic in his voice. "Where are you?"

"Trying to get back towards your apartment..." Then everything went black.

/

Booth POV

I was surprised to see Bones number light up my cell phone.

"Bones?"

"Booth! I am being chased." Holy shit!

"What?" Not good. Who would chase her? How do I help her? "Where are you?" Please be close.

"Trying to get back towards your apartment..." I hear gunfire in the background and the sound of crunching metal not just through the phone. I can hear it out front. I grab my gun and run out to the street. I see a black town car speed away. I fire at the car and am able to catch the plate.

"Agent Booth, I need an ambulance and team to my location. We have an officer down."

Her car was smashed into a telephone pole and she was slumped over the steering wheel. I pulled at the door and it finally opened. She was shot. I gently pulled her from the car and laid her on the ground. I know you aren t supposed to move a victim but she was loosing too much blood. I felt her neck for a pulse, it was faint. Her breathing was shallow.

"Stay with me Bones." I took off my shirt, pressing it into the shot in her chest. "Come on. Think of Kat. Stay with me." No response. I could hear the sirens, they were close. This can't happen. I can't loose her now.

The FBI Team arrived first. Cullen was with them.

"Booth what the hell happened?" I cannot believe he is on me right now, while she is bleeding out in my hands.

"She called and told me she was being chased. She was able to get back towards my place. I heard shots and the crash. I caught the plate PAZ429F. Where the hell is the ambulance?"

"I will put someone on the plate. They are pulling up." I ignored him, my only focus was Bones. The medics came over and immediately removed me from her. I heard them calling out medical stats back and forth my mind was a jumble. They loaded her on a gurney and rolled her to the ambulance. I climbed up into the ambulance with them, as they closed the doors her heart stopped.

"We lost her. Need epi! Charging paddles." They injected her with something and pulled open her shirt. "Clear!" They shocked her and her heart rate jumped and then dropped. "Charging 360 clear!" They shocked her again. "Got her!" I just sat there and prayed. When we arrived at the hospital they wheeled her into the ER with me right behind. There was a flurry of activity till they finally threw me out of the room.

I stood in the hall. I have to call Angela. I was covered in her blood. The thought made me sick. I pulled out my cell to call Ang.

"Hello?"

"Angela it's Booth."

"What's wrong?" Bless that woman for knowing by my voice.

"I am at the hospital. Bones was shot."

"What? What the hell happened? She was suppose to be on a plane now." I could hear her voice cracking.

"She came to see me at the apartment, told me about Kat." Now my voice was cracking. "She had left and was on her way to the airport. She called me and told me she was being followed. She made it back in front of my place when I heard the shots and the crash."

"Oh my god! Is she going to be alright?" Angela was now crying. I could hear Jack asking what was going on in background.

"Honestly I don't know. They lost her once on the way here." I bit back a sob but I knew she heard it. "They are working on her now."

"We will be there as soon as we can."

"Ang! Don't hang up yet." i paused "When you come act as though Kat is yours. I don't know who is after her and I don't want Kat in danger."

"Done."

Now I just had to sit here and wait for word on her condition. Please let her be alright. I can't lose her. Kat can't lose her.


	16. Chapter 16

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

_**Booth POV**_

I am just sitting here praying she is ok. I also can't help but to keep thinking of the conversation we had before she left. We have a daughter. I don't know how long I have been sitting here but it feels like days.

"Family of Temperance Brennan?"

"Yes. Here." I jump up.

"You are?" Oh crap...

"Fiancee. How is she?"

"She is still in surgery. I wanted to come out and update you. Also per her records, Angela Montenegro is her medial proxy. I need to reach her."

"She is probably on a plane here. Um hold on." I dialed the phone putting it on speaker phone.

"Booth? We are almost there." Angela sounded frantic.

"Ang the doctor is here with me. You are her proxy."

"Yes. Doctor?"

"Mrs. Montenegro, Temperance has suffered multiple gunshots. One to the shoulder which is minor, but the other was to the chest. The bullet grazed the aorta and did severe damage to the left lung."

"Oh god." Angela was crying again.

"We need to stop her heart completely and put her on bypass in order to repair the damage."

"What is bypass?" I asked before Angela could.

"We would stop her heart and put feeds into her body to push blood through systems to avoid damage to other organs. This would keep her alive while we work on heart and lung. There is a risk that her heart won't restart but at this point we do not have another option."

"Do it. Do whatever you need to in order to save her. My husband and I will be there within the hour. Agent Booth can speak in our place if you cannot reach us."

The doctor left and went back to work on Bones. Now I was back to sitting here alone praying. What will happen if I lose her? What about Kat? I never even met her. All of this is my fault. If I hadn't...oh god...if I hadn't slept with Sam this wouldn't be happening. I would have known about Kat. I could have been home for her birth. I would have been with her and she wouldn't have been alone.

"Booth?" I looked up, it was Ang and Jack. She was holding Kat. How long was I sitting here?

"Hey. No word yet. She is still in surgery." Ang and Jack sat across from me. Ang was still holding Kat who looked to be sleeping. From what I could see she was gorgeous.

None of us were saying anything. We sat in silence. We all knew this wasn't the place to bring up anything. Out focus was on Bones and I didn't want to upset either of them. Kat was peaceful in Angela's arms and I didn't want to disturb her. Everything in me was screaming to hold her.

I was lost in thought staring at Kat. It had to have been 5 hours when we finally heard something.

"Family of Temperance Brennan?"

"Doc. Over here." I was relieved to see it was the same doctor. "We were able to repair the damage to the heart and lungs. We were able to take her off of bypass and restart her heart function." I let out a breath I didn't realize I had been holding. "There has been a complication. She has fallen into a coma. More then likely due to the trauma she sustained. Honestly we were surprised she pulled through. We need to monitor her closely for the next 48 hours."

"Can we see her?" I was trying hard to not show how upset I am.

"As soon as she is out of recovery, I will have a nurse come and show you to her room."

"Thank you." Ang finally said something, her eyes were full of tears. Kat stirred and opened her eyes. "Hear that baby girl. Your mama is doing better." Jack was holding Ang and smiling at Kat. I couldn't help the jealously of his closeness to my daughter. Jack looked up and saw me watching him.

"Booth. Do you want to hold her?" I was shocked. Angela looked angry.

"Yes...please." I know I whispered it but I was so grateful and broken right now.

Jack took Kat from Angela and handed her to me. I lifted her into my arms and those gorgeous eyes that looked just like Bones stared back at me. She watched me, just like Bones analyzed bones.

"Hey baby girl." She let out a blabbing giggle, which brought more tears to my eyes. "You are gorgeous just like your mama." She waved her fingers at me. I kissed her on the forehead and just held her. I didn't want to push it with Angela and Jack so I graciously handed her back. She nestled back against Ang and fell back to sleep. Now we just had to continue to wait to be able to visit Bones.


	17. Chapter 17

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture until the new season is back!

/

_**Booth POV**_

Angela and Jack let me go in first. She looked so pale, there were wires and tubes going everywhere. If it wasn't for the steady beep of the heart monitor, you wouldn't know she was alive. I choked back a sob and walked over to her side. I gently took her hand in mine and help it to my lips.

"Bones." I knew my voice was cracking. "You can't leave us. Me. I need you."

I looked up and Angela was standing there. From the look on her face, I knew she heard what I said. I just continued to hold Bones hand and went back to talking to her. I didn't care now what Ang thought this is where I needed to be.

"I met Kat. She is gorgeous, just like her mother. She analyzed me like you do remains." I laughed through tears. "Angela and Jack are here. We really need you to be ok." I couldn't do it anymore I just held her hand and cried.

**_Angela POV_**

"Bones." His voice was cracking. "You can't leave us. Me. I need you." He looked like hell. He loved her. He still loved her. What the hell happened then? How did we all get here? He went back to talking to her ignoring me.

"I met Kat. She is gorgeous, just like her mother. She analyzed me like you do remains." He laughed through tears. "Angela and Jack are here. We really need you to be ok." Booth continued to hold Brennan's hand and placed his head down on the bed and sobbed. For as mad as I was at him for all he put Bren through, it broke my heart to hear him. I knew he regretted whatever that was with that woman. I knew when he explained to me on the phone, but I was so angry for what he put Bren through. I let him be. I sat at the other side of the bed and just started talking to her.

"Heya Sweetie... you really know how to get my attention. I think Jack and I broke airspeed laws getting here when Booth called us. Kat is here she is fine. Jack is watching her right now. I didn t think it was a good idea to bring her in here. You need to get yourself better so you don't frighten her." I ran my fingers in her hair. "Come on sweetie, you really need to get better here. No pressure or anything." I tried to keep my voice light and positive even though I feared the worst. She looked horrible.

Jack and I had a hotel nearby. Booth wouldn't leave. The nurses brought a cot in for him even though I doubt he would ever leave that chair. Cullen had come by to update us, Booth ignored and just stayed by Bren. They had a suspect and an all alert bulletin out on him. I hope they killed him instead of catching him. It was hard to believe I thought it but god look at her.

_**Booth POV**_

It s been three days nothing. No change in condition. The doctors said next 48 hours were critical. It has been over 72. The longer she is unconscious the less likely she is to wake up. As each hour passes, my hope, my heart and my body shatter with her. I love her with everything I am. Even though I have Parker and Kat, I do not want to know life without her.

"Come on Bones. I am begging you to give me some sign you are still in there. I love you..." I had tears down my face and was holding her hand.

I felt her fingers loosely wrapped around my hand

"Bones?"


	18. Chapter 18

**Misunderstandings**

Disclaimer: I do not own Bones. I am making nothing from this, but my own enjoyment and torture until the new season gets interesting again.

Authors Note: I apologize for the delayed update. Honestly since my friends sudden death a few months ago, I have just not been able to get myself in writing mode. I am trying. Please be patient, I will finish this story. To be really honest, I was hoping the new season would inspire me a bit more to get me back into this. I am finding this season has been less then inspriational and more frustrating then anything else. I hate to say it, but the plot is completely turning me off. I haven't even watched last episode its sitting in my dvr waiting.

**Brennan POV**

"Come on Bones. I am begging you to give me some sign you are still in there. I love you..." I could head Booth, but his voice sounded so far away.

I felt something on my hand, I tried to move my fingers.

"Bones?" Booth again, I must of moved one of them. "That's it. Come back to us. Kat wants her mom back." That did it. I focused hard and gripped his hand.

I forced my eyes to open but they felt so unbelievably heavy. As they opened, I could see Booth's worried tear streaked face looking at me.

**Booth POV**

"Come on Bones. I am begging you to give me some sign you are still in there. I love you..." I felt her fingers move.

"Bones?" I was pleading and I didn't care even if she woke up only to throw me out. "That s it. Come back to us. Kat wants her mom back." That did it. She opened her eyes and was staring right at me.

"Hey. Easy." I squeezed her hand to assure her. "We are at DC General. They patched you up, we have just been waiting for you to wake up. Angela, Jack and Kat are here."

"Did you get them?" Her voice was music to my ears. It was but a whisper, but it was beautiful.

"No. By the time I got downstairs you were already shot and they were driving off." I looked her in the eyes so she understood. "My priority was you."

"Thank you." she smiled slightly at me and gave my hand the softest squeeze. "Is Kat here?" I couldn't help but smile at that.

"Yes but Jack and Angela too her with them to hotel to get some rest. Their daughter was getting cranky." She looked at me confused. I leaned over and whispered in her ear. "It's for her protection nobody knows she is ours until we find whoever did this." I kissed her cheek and pulled away. Our eyes locked and I knew she understood.

"Can you get Doctor in here so I can hear about all my injuries?" I rolled my eyes but smiled.

She was back! I got up and went to nurses station to let them know she was awake and asking for the Doctor.


	19. Chapter 19

Misunderstandings

Disclaimer: I do not own Bones. I am making nothing from this but my own enjoyment and torture. Now this is turning into more of an outlet for my displeasure with the new season! Ugh!

Authors Note: Thank you all for the reviews, adding of story to favorites and alerts. Good to see and is snapping me out of my funk. :)

Brennan POV

"Dr. Brennan. Good to see you awake. You had everyone worried for a bit."

"Can you tell me everything you did and what is wrong? Additionally, how long till I can leave?" I wanted out of here. As Hodgins would say, I felt like a sitting duck. I could see Booth smirking, he knew I would ask. Which irrationally makes me want to smack and hug him. Angela truly is rubbing off on me.

"Yes of course. You had two gunshot wounds. One to shoulder, which was minor. No damage to bones just flesh. The other bullet nicked your aorta and damaged your lung. We placed you on bypass while we repaired the damage. Due to trama you inflicted you have been in a coma the last several days."

"Any risk of further complications?"

"You have only been out of surgery a few days. With damage to heart and lung we really want to keep you on observation and minimal activity."

"How long?" I was getting very frustrated with this doctor. The doctor looked to Booth for help. "He is not my keeper. How long?"

"3 days minimum unless you have complications in interim."

"Thank you." The doctor practically ran from the room.

"Bones, you really need to take it easy." His eyes were tear-filled which surprised me. "They lost you once in the ambulance. I almost lost you." Tears spilled from his eyes and I was lost.

"I do not plan to harm myself Booth. I have Kat to worry about."

"She's beautiful." His voice cracked.

"Yes she is, but can you really be surprised with her parents." I smiled at him and he laughed.

"I am sorry Bones."

"Booth...I know, but there is a lot that has happened."

"I know Bones, one day at a time. Just don't shut me out is all I ask."

I nodded and in truth I could deny him nothing. He was my Achilles heel.


End file.
